They count by keeping track of the user-agent string in the http headers sent when a web user requests one of WebSideStory's transparent tracking GIFs. These tracking images are embedded, much like ads, in some web pages. IMO, Firefox users are more likely than IE users to block these images for privacy reasons, which would lead to a disproportionate percentage of IE users requesting the tracking images. Thus we can assume that Firefox enjoys a higher user share than WebSideStory reports.